MIAMI—Concerns over rising sea levels and floods are beginning to reshape one of the country’s largest housing markets, with properties closer to sea level now trading at discounts to those at higher elevations.

Research published Friday in the journal of Environmental Research Letters shows that single-family homes in Miami-Dade County are rising in value more slowly near sea level than at higher elevations, as buyers weigh the possibilities of more-frequent minor flooding in the short term and the challenge of reselling...